This is a very common situation. While we have not done this specific excursion, our family of 3 has done a number of guided kayak tours across the country, always with 2-person kayaks, and it has never been a problem. Our 3rd person is always paired with the guide or a solo traveler or the odd person from another group. With an even number of travelers, the tour guide might take a single kayak, but I cannot remember any time another guest in our tour group was asked or allowed to take a single.
FWIW, Another site that appears to be selling the same sort of excursion (AK travel adventures) says "...you will board the two-person kayaks, with either a new friend or traveling companion, and set off on your Alaskan adventure."